RNA interaction format: a general data format for RNA interactions.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2023
01 11 2023
Historique:
received:
29
11
2022
revised:
19
09
2023
medline:
14
11
2023
pubmed:
9
11
2023
entrez:
9
11
2023
Statut:
ppublish
Résumé
RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardized data format that can capture the nature of all these different interactions in detail. Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA-RNA and RNA-Protein interactions and provide reference implementations in C/C++, Python, and JavaScript. RIF is released under licence GNU General Public License version 3 (GNU GPLv3) and is available on https://github.com/RNABioInfo/rna-interaction-format.
Identifiants
pubmed: 37944046
pii: 7379667
doi: 10.1093/bioinformatics/btad665
pmc: PMC10640394
pii:
doi:
Substances chimiques
RNA
63231-63-0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D248-53
pubmed: 26503244
Genome Biol. 2014 Jan 22;15(1):R17
pubmed: 24451197
Bioinformatics. 2023 Apr 3;39(4):
pubmed: 37042720
Nat Biotechnol. 2010 Sep;28(9):935-42
pubmed: 20829833
J Integr Bioinform. 2018 Mar 9;15(1):
pubmed: 29522418
Nucleic Acids Res. 2020 Jan 8;48(D1):D220-D225
pubmed: 31598696
J Mol Biol. 2022 Jun 15;434(11):167530
pubmed: 35662463
Algorithms Mol Biol. 2006 Mar 16;1(1):3
pubmed: 16722605
Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154
pubmed: 31647101
Genome Biol. 2005;6(5):R44
pubmed: 15892872
Nucleic Acids Res. 2021 Jun 4;49(10):5493-5501
pubmed: 34019662
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Nat Biotechnol. 2004 Feb;22(2):177-83
pubmed: 14755292
Nucleic Acids Res. 2018 Jan 4;46(D1):D194-D201
pubmed: 29040625